debian/0000755000000000000000000000000011755204706007175 5ustar debian/libjgromacs-java.classpath0000644000000000000000000000006511755204704014313 0ustar usr/share/java/jgromacs.jar /usr/share/java/jama.jar debian/watch0000644000000000000000000000015611755204140010220 0ustar version=3 opts="uversionmangle=s/$/.0/" \ http://nanomed.bioch.ox.ac.uk/jgromacs/ jgromacs_v([\d.]+)_src.tgz debian/libjgromacs-java.jlibs0000644000000000000000000000001511755204140013421 0ustar jgromacs.jar debian/control0000644000000000000000000000455111755204140010575 0ustar Source: jgromacs Section: science Priority: extra Maintainer: Debichem Team Uploaders: Steffen Moeller Build-Depends: debhelper (>> 8), default-jdk, javahelper, libjama-java Standards-Version: 3.9.3 Homepage: http://nanomed.bioch.ox.ac.uk/jgromacs/ Vcs-Svn: svn://svn.debian.org/svn/debichem/unstable/jgromacs Vcs-Browser: http://anonscm.debian.org/viewvc/debichem/unstable/jgromacs Package: libjgromacs-java Architecture: all Section: java Depends: ${java:Depends}, ${misc:Depends} Suggests: gromacs | gromacs-openmpi, libjgromacs-java-doc Description: library for molecular dynamics trajectory analysis JGromacs is a Java library designed to facilitate the development of cross-platform analysis applications for Molecular Dynamics (MD) simulations. The package contains parsers for file formats applied by GROMACS (GROningen MAchine for Chemical Simulations), one of the most widely used MD simulation packages. . JGromacs provides a multilevel object-oriented representation of simulation data to integrate and interconvert sequence, structure and dynamics information. In addititon, a basic analysis toolkit is included in the package. The programmer is also provided with simple tools (e.g. XML-based configuration) to create applications with a user interface resembling the command-line UI of Gromacs applications. Package: libjgromacs-java-doc Architecture: all Section: doc Depends: ${java:Depends}, ${misc:Depends} Recommends: ${java:Recommends} Description: library for molecular dynamics trajectory analysis (documentation) JGromacs is a Java library designed to facilitate the development of cross-platform analysis applications for Molecular Dynamics (MD) simulations. The package contains parsers for file formats applied by GROMACS (GROningen MAchine for Chemical Simulations), one of the most widely used MD simulation packages. . JGromacs provides a multilevel object-oriented representation of simulation data to integrate and interconvert sequence, structure and dynamics information. In addititon, a basic analysis toolkit is included in the package. The programmer is also provided with simple tools (e.g. XML-based configuration) to create applications with a user interface resembling the command-line UI of Gromacs applications. . This package contains the documentation for libjgromacs-java. debian/source/0000755000000000000000000000000011754733370010500 5ustar debian/source/format0000644000000000000000000000001411754733370011706 0ustar 3.0 (quilt) debian/changelog0000644000000000000000000000023111754733370011046 0ustar jgromacs (1.0-1) unstable; urgency=low * Initial release (Closes: #673139) -- Steffen Moeller Wed, 16 May 2012 14:12:46 +0200 debian/copyright0000644000000000000000000000310211755204140011114 0ustar Format: http://dep.debian.net/deps/dep5 Upstream-Name: jgromacs Source: http://nanomed.bioch.ox.ac.uk/jgromacs/ Files: jgromacs/* Copyright: 2011 Márton Münz and Dr. Philip C Biggin License: GPL-3.0+ Files: jama/* Copyright: none License: public-domain This software is a cooperative product of The MathWorks and the National Institute of Standards and Technology (NIST) which has been released to the public domain. Neither The MathWorks nor NIST assumes any responsibility whatsoever for its use by other parties, and makes no guarantees, expressed or implied, about its quality, reliability, or any other characteristic. Files: debian/* Copyright: 2012 Steffen Moeller 2012 Debichem Team License: GPL-3.0+ License: GPL-3.0+ This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. . This package is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. . You should have received a copy of the GNU General Public License along with this program. If not, see . . On Debian systems, the complete text of the GNU General Public License version 3 can be found in "/usr/share/common-licenses/GPL-3". debian/compat0000644000000000000000000000000211755204140010363 0ustar 8 debian/patches/0000755000000000000000000000000011755204140010614 5ustar debian/patches/series0000644000000000000000000000001711754733370012042 0ustar jamaJama.patch debian/patches/jamaJama.patch0000644000000000000000000000551511755204140013344 0ustar Author: Steffen Moeller Description: Build with Debian jama library A consequence of building with the system jama. The debian package has the class hierarchy starting with an upper case 'Jama' rather than the 'jama' directory this source tree shipped the JAMA library in. --- a/jgromacs/analysis/Distances.java +++ b/jgromacs/analysis/Distances.java @@ -33,7 +33,7 @@ import jgromacs.data.Residue; import jgromacs.data.Structure; import jgromacs.data.Trajectory; -import jama.Matrix; +import Jama.Matrix; /** --- a/jgromacs/analysis/Angles.java +++ b/jgromacs/analysis/Angles.java @@ -25,7 +25,7 @@ import java.util.ArrayList; -import jama.Matrix; +import Jama.Matrix; import jgromacs.data.Angle; import jgromacs.data.Point3D; --- a/jgromacs/analysis/Dynamics.java +++ b/jgromacs/analysis/Dynamics.java @@ -30,8 +30,8 @@ import jgromacs.data.PointList; import jgromacs.data.Structure; import jgromacs.data.Trajectory; -import jama.EigenvalueDecomposition; -import jama.Matrix; +import Jama.EigenvalueDecomposition; +import Jama.Matrix; /** * Collection of methods for analysing molecular motions --- a/jgromacs/analysis/GNM.java +++ b/jgromacs/analysis/GNM.java @@ -23,8 +23,8 @@ package jgromacs.analysis; -import jama.Matrix; -import jama.SingularValueDecomposition; +import Jama.Matrix; +import Jama.SingularValueDecomposition; import java.util.ArrayList; --- a/jgromacs/analysis/Similarity.java +++ b/jgromacs/analysis/Similarity.java @@ -29,7 +29,7 @@ import jgromacs.data.PointList; import jgromacs.data.Structure; import jgromacs.data.Trajectory; -import jama.Matrix; +import Jama.Matrix; /** * Collection of methods for measuring structural similarity --- a/jgromacs/analysis/Superposition.java +++ b/jgromacs/analysis/Superposition.java @@ -30,8 +30,8 @@ import jgromacs.data.PointList; import jgromacs.data.Structure; import jgromacs.data.Trajectory; -import jama.Matrix; -import jama.SingularValueDecomposition; +import Jama.Matrix; +import Jama.SingularValueDecomposition; /** * Collection of methods for superposing structures --- a/jgromacs/data/Point3D.java +++ b/jgromacs/data/Point3D.java @@ -23,7 +23,7 @@ package jgromacs.data; -import jama.Matrix; +import Jama.Matrix; /** * Objects of this class represent a single 3D point --- a/jgromacs/data/PointList.java +++ b/jgromacs/data/PointList.java @@ -25,7 +25,7 @@ import java.util.ArrayList; -import jama.Matrix; +import Jama.Matrix; /** * Objects of this class represent a list of 3D points --- a/jgromacs/io/IOMath.java +++ b/jgromacs/io/IOMath.java @@ -31,7 +31,7 @@ import java.io.IOException; import java.util.ArrayList; -import jama.Matrix; +import Jama.Matrix; /** * This class contains static methods for IO of ArrayList and Matrix objects debian/rules0000755000000000000000000000104111755204443010247 0ustar #!/usr/bin/make -f # -*- makefile -*- # Sample debian/rules that uses debhelper. # This file was originally written by Joey Hess and Craig Small. # As a special exception, when this file is copied by dh-make into a # dh-make output file, you may use that output file without restriction. # This special exception was added by Craig Small in version 0.37 of dh-make. # Uncomment this to turn on verbose mode. #export DH_VERBOSE=1 export JAVA_HOME=/usr/lib/jvm/default-java export CLASSPATH=/usr/share/java/jama.jar %: dh $@ --with=javahelper debian/debhelper.log0000644000000000000000000000005511755031044011623 0ustar dh_auto_configure dh_auto_build dh_auto_test debian/javabuild0000644000000000000000000000002611755204140011047 0ustar jgromacs.jar jgromacs debian/upstream0000644000000000000000000000067311755030621010757 0ustar Name: JGromacs Homepage: http://nanomed.bioch.ox.ac.uk/jgromacs Reference: - Author: Márton Münz and Philip C. Biggin Title: "JGromacs: A Java Package for Analyzing Protein Simulations" Journal: J. Chem. Inf. Model. Year: 2012 Volume: 52 Number: 1 Pages: 255-259 URL: http://pubs.acs.org/doi/abs/10.1021/ci200289s eprint: http://pubs.acs.org/doi/pdfplus/10.1021/ci200289s PMID: 22191855 DOI: 10.1021/ci200289s debian/libjgromacs-java-doc.javadoc0000644000000000000000000000001111755204140014464 0ustar internal